View source for Cloning 7 casein gBlocks, 12Sep2014 and on

= Cloning 7 casein gBlocks into pD1214, transforming into ''E. coli'' and extracting plasmid DNA=

== Overview ==

During this series of experiments, we will insert seven casein gene constructs (detailed below) into the pD1214 vector and transform our seven constructs into ''E. coli.'' We will then perform a midiprep plasmid DNA extraction, quantify our plasmid DNA, and submit all seven constructs for sequencing. Sequence-confirmed DNA is then ready to be transformed into yeast.

'''Casein constructs'''

1) P.FAKS.bovAlphaS1.S
 
2) P.FAKS.bovAlphaS2(Kex-).S

3) P.FAKS.bovAlphaS2(Kex+).S 

4) P.FAKS.humBeta.S 

5) P.FAKS.humKappa(Kex-).S 

6) P.FAKS.Beta(A2).S (bov) 

7) P.FAKS.bovKappa.S 

*These gBlock sequences have 5' and 3' SapI sequences, followed by full length FAKS, followed by the human or bovine casein gene of interest. Electra cloning cleaves at SapI sites and ligates simultaneously. 

*We cloned into pD1214. This vector was ordered from DNA2.0 and is linearized upon arrival. Our insert is treated with Electra enzyme mix which cuts and ligates our "SapI.gene.SapI" and inserts it into the pD1214 vector.

*SapI treated DNA has an ATG overhang at the 5' end and a GGT overhang at the 3' end. Our complete vector will have the alphafactorfull signal sequence, which leads into another Methionine (M), followed by the rest of the human kappa casein protein.

[https://www.dna20.com/products/expression-vectors/electra-system#2 All you need to know about the Electra system.]

== Cloning casein gBlocks into pD1214 ==

'''September 12, 2014'''

*'''Participants:''' Advait, Patrik, Johan, Meenakshi, Rachel, Lafia, Nikola, Moises, Aaron, Wes, Arif

*'''Notes:''' Rachel

*'''Location:''' BioCurious

*'''Materials & Methods, Electra Cloning:'''
**We resuspended all lyophilized IDT gBlock DNA as in [[DNA Handling]] using 0.5X TE (1X TE, pH 7.5: 1 diH2O). Final DNA concentration = 20ng/uL, per Electra cloning kit requirements.
** Used  [https://www.dna20.com/products/expression-vectors/electra-system#2 DNA 2.0 Electra cloning kit] protocol.
**Completed 8 separate reactions, one for each gBlock and one positive control using DNA supplied in the kit. 
**5uL reaction products used immediate for transformation into ''E. coli,'' below. Remainder stored at -20°C, BioCurious freezer. Each tube labeled with date and casein construct ID.

Reaction: 
 1uL pD1214 (20ng)
 1uL (20ng) of appropriate casein gBlock or (+) control DNA 
 2uL Electra Buffer
 1uL of Electra enzyme mix
 15uL of Water
 ----
 20uL, Room Temperature, 20min.

==Transforming cloning reaction products into ''E. coli'' ==

'''September 12, 2014'''

*'''Participants:''' Advait, Patrik, Johan, Meenakshi, Rachel, Lafia, Nikola, Moises, Aaron, Wes, Arif

*'''Notes:''' Rachel

*'''Location:''' BioCurious

*'''Materials & Methods, Transforming ''Mix & Go'' Competent dH5alpha ''E. coli'' with gBlocks in pD1214, above:'''
**We used the Zymo Research instruction manual for "Premade Mix & Go Competent ''E. coli'' Cells." [[Media:Zymo_E._coli_competent_cells_transformation_protocol.pdf‎]]
**We completed 10 reactions: one for each of the 8 Electra cloning reactions, one pGLO positive control, one diH2O negative control.
***Thawed individual tubes of ''Mix & Go'' chemically competent, dH5alpha ''E. coli'' cells slowly on ice.
***Prewarmed LB agar plates with Carb-50, 100mm (Teknova), at 37°C.
***Added 5uL of each casein:pD1214 or appropriate control to individual thawed tube of 100uL competent cells. Mixed gently.
***Immediately incubated on ice for 10 min.
***Plated 100uL of each reaction to LB carb plates, using one individualy wrapped spreader/reaction. 
****Inducible promoter for pGLO positive control requires arabinose, so 200uL of arabinose spread onto that LB carb plate prior to transformation mix being spread.
***Incubated plates overnight at 37°C.

'''September 14, 2014'''
*'''Results:'''
**All casein:pD1214 --> dH5alpha ''E. coli'' transformation reactions yielded colonies on LB carb ''EXCEPT'' P.FAKS.humBeta.S. Few colonies for P.FAKS.humKappa(Kex-).S, and multiple colonies on remaining successful plates, 
**Positive and negative control plates as expected.
*'''Future Directions:''' We will proceed to extract the plasmid DNA from successful transformations. We will also troubleshoot failed P.FAKS.humBeta.S transformation: all further notes in [[Troubleshooting failed 12Sep2014 transformation of P.FAKS.humBeta.S]].

==Plasmid midipreps of successful 12Sep2014 transformations==
'''September 14, 2014'''

*'''Participants:''' Johan, Patrik, Aaron, Meenakshi

*'''Location:''' BioCurious

*'''Aims:''' Extract the plasmid DNA from the six successful IDT gBlock:pD1214 to dH5alpha transformations (September 12, 2014) using the Zyppy Plasmid  Midiprep kit. After quatification, we will submit this DNA for sequencing prior to working with it in yeast.

Casein constructs in pD1214 vector we will be midi-prepping today: 

1) P.FAKS.bovAlphaS1.S
 
2) P.FAKS.bovAlphaS2(Kex-).S

3) P.FAKS.bovAlphaS2(Kex+).S 

5) P.FAKS.humKappa(Kex-).S 

6) P.FAKS.Beta(A2).S (bov) 

7) P.FAKS.bovKappa.S

*'''Materials and Methods:'''
**We used the Zyppy Plasmid Midiprep Kit (Protocol = [[Media:D4025i.pdf‎]]): 
*** Followed "Centrifugation Protocol" stream with the following specific changes to step 1): grew in 12mL of LB Carb [''need carbenicillin concentration''] and added 6mL of water to the bacterial cell pellet. 
**Midiprepped DNA is stored in Johan's pink box at -20°C in the freezer at BioCurious.

==Plasmid DNA quantification & purity spec readings for 14Sep2014 midipreps==
'''September 16,2014'''

*'''Participants:''' Aaron, Meenakshi, Johan, Lafia, Matt

*'''Location:''' BioCurious

*'''Aims:''' DNA quantification of all midipreped sample by using spectrophotometer.

*'''Materials and Methods:'''
We used 1:10 dilution. Sample no 3 ( P. FAKS. Bovine alpha ( Kex +).s had shown less concentration because in 1 tube from duplicate set had less growth during midiprep.

Sample.                                               260nm.                       280nm.                  260/280.                      micro g / ml   

1.                                                          0.0748.                     0.0043.                      1.8546.                        37.416     

2.                                                           0.0412.                     0.0240.                     1.7177.                         20.616

3.                                                           0.0174.                      0.0095.                     1.8264.                        0.8688

5.                                                           0.0479.                      0.0256.                     1.8697.                        23.935

6.                                                            0.0316.                      0.0148.                    2.1362.                        15.819

7.                                                             0.0693.                     0.0342.                    2.0245.                        34.632